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    	<title>Names on Nodes</title>
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		<meta name="Author" content="T. Michael Keesey" />
		<meta name="Description" content="Names on Nodes, a web application that performs the automatic application of biological nomenclature." />
		<meta name="Keywords" content="names,nodes,Keesey,Mike,Michael,biological,biology,hierarchy,nomenclature,code,phylogeny,phylogenetic,rank,based" />
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			<h1><span class="title">Names on Nodes</span></h1>
			<p class="subtitle">automated application of biological nomenclature</p>
			<h2>Applications</h2>
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						<a href="./app/" class="icon">
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						<p>
							<span class="app-title title">Names on Nodes</span> is a web application that automatically applies biological nomenclature to datasets.
							Datasets may be loaded as bioinformatics files (currently <span class="langname">Newick</span> and <span class="langname">NexML</span>).
							<span class="title">Names on Nodes</span> uses the mathematical definitions of names to apply them to phylogenetic hypotheses.
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						<p>
							The basic principles which <span class="title">Names on Nodes</span> uses were laid out in:
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						<ul>
							<li>
								<span class="citation-authors">Keesey, T. M.</span> (2007 Sep 21).
								A mathematical approach to defining clade names, with potential applications to computer storage and processing.
								<span class="title">Zoologica Scripta</span>
								<span class="volume-number">36</span>(6):607&ndash;621.
								<a href="http://dx.doi.org/10.1111/j.1463-6409.2007.00302.x"><code>doi:10.1111/j.1463-6409.2007.00302.x</code></a>
							</li>
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						<p>
							Currently <span class="title">Names on Nodes</span> is in a public alpha phase.
							The project has a <a href="http://bitbucket.org/keesey/namesonnodes-sa">BitBucket page</a> where you can <a href="http://bitbucket.org/keesey/namesonnodes-sa/issues/new/">report issues</a>, <a href="http://bitbucket.org/keesey/namesonnodes-sa/issues/new/">request features</a>, and check out the source code (using <a href="http://mercurial.org/">Mercurial</a>).
							Progress can be followed at Mike Keesey's blog, <a href="http://3lbmonkeybrain.blogspot.com/search/label/Names%20on%20Nodes" class="title">A Three-Pound Monkey Brain</a>.
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						<p>
							Older <span class="title">Names on Nodes</span> projects (also incomplete) are housed on <span class="title">Google Code</span>, here: <a href="http://code.google.com/p/namesonnodes/"><code>http://code.google.com/p/namesonnodes/</code></a>.
							The <span class="title">Google Code</span> repository also houses all versions of this website.
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						<div class="link">
							<a href="./app/">Open <span class="title">Names on Nodes</span> &rarr;</a>
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						<a href="./texttree/" class="icon">
							<img src="./images/texttree.png" width="150" height="90" alt="Text Tree Maker"/>
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						<p>
							<span class="app-title title">Text Tree Maker</span> converts Newick tree strings into readable text cladograms.
						</p>
						<div class="link">
							<a href="./texttree/">Open <span class="title">Text Tree Maker</span> &rarr;</a>
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						<a href="./phylopainter/" class="icon">
							<img src="./images/phylopainter.png" width="150" height="90" alt="PhyloPainter"/>
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						<p>
							<span class="app-title title">PhyloPainter</span> converts Newick tree strings into cladograms using an HTML 5 <code>&lt;canvas&gt;</code> object.
						</p>
						<div class="link">
							<a href="./phylopainter/">Open <span class="title">PhyloPainter</span> &rarr;</a>
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			<h2>Documentation</h2>
			<h3><span class="langname">MathML</span> Definitions</h3>
			<p>
				<span class="title">Names on Nodes</span> uses <a href="http://www.w3.org/TR/MathML2/" class="langname">MathML 2.0</a> to model nomenclatural definitions.
				To accomplish this, it relies on certain mathematical entities related to phylogeny.
				These are defined and discussed in the <a href="./ns/math/2009/index.html"><span class="title"><span class="langname">MathML</span> Definitions</span> document</a>.
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